scholarly journals Molecular identification of Nocardia species causing endophthalmitis using multilocus sequence analysis (MLSA): a 10-year perspective

2020 ◽  
Vol 69 (5) ◽  
pp. 728-738 ◽  
Author(s):  
Hariharan Gnanam ◽  
Siva Ganesa Karthikeyan Rajapandian ◽  
Rameshkumar Gunasekaran ◽  
Swasthikka Roshni Prithiviraj ◽  
Ram Sudarshan Ravindran ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Molecular Identification ◽  
Multilocus Sequence Analysis ◽  
Nocardia Species

scholarly journals Antimicrobial Susceptibility among Clinical Nocardia Species Identified by Multilocus Sequence Analysis

2014 ◽  
Vol 59 (1) ◽  
pp. 269-275 ◽  
Author(s):  
Lisa R. McTaggart ◽  
Jennifer Doucet ◽  
Maria Witkowska ◽  
Susan E. Richardson
Keyword(s):  
Sequence Analysis ◽  
Antimicrobial Susceptibility ◽  
Multilocus Sequence Analysis ◽  
Nocardia Species ◽  
Content Type ◽  
Clinical Specimens ◽  
Nocardia Otitidiscaviarum ◽  
Species Specific ◽  
Susceptibility Profiles ◽  
First Time

ABSTRACTAntimicrobial susceptibility patterns of 112 clinical isolates, 28 type strains, and 9 reference strains ofNocardiawere determined using the Sensititre Rapmyco microdilution panel (Thermo Fisher, Inc.). Isolates were identified by highly discriminatory multilocus sequence analysis and were chosen to represent the diversity of species recovered from clinical specimens in Ontario, Canada. Susceptibility to the most commonly used drug, trimethoprim-sulfamethoxazole, was observed in 97% of isolates. Linezolid and amikacin were also highly effective; 100% and 99% of all isolates demonstrated a susceptible phenotype. For the remaining antimicrobials, resistance was species specific with isolates ofNocardia otitidiscaviarum,N. brasiliensis,N. abscessuscomplex,N. novacomplex,N. transvalensiscomplex,N. farcinica, andN. cyriacigeorgicadisplaying the traditional characteristic drug pattern types. In addition, the antimicrobial susceptibility profiles of a variety of rarely encountered species isolated from clinical specimens are reported for the first time and were categorized into four additional drug pattern types. Finally, MICs for the control strainsN. novaATCC BAA-2227,N. asteroidesATCC 19247T, andN. farcinicaATCC 23826 were robustly determined to demonstrate method reproducibility and suitability of the commercial Sensititre Rapmyco panel for antimicrobial susceptibility testing ofNocardiaspp. isolated from clinical specimens. The reported values will facilitate quality control and standardization among laboratories.

Multilocus Sequence Analysis and Copper Ion Resistance Detection of 60 Xanthomonas arboricola pv. juglandis Isolates from China

Plant Disease ◽  
2021 ◽  
Author(s):  
Benzhong Fu ◽  
Jieqian Zhu ◽  
Conard Lee ◽  
Lihua Wang
Keyword(s):  
Sequence Analysis ◽  
Copper Ion ◽  
Housekeeping Genes ◽  
Threshold Value ◽  
Pcr Primers ◽  
Multilocus Sequence Analysis ◽  
Nucleotide Polymorphisms ◽  
Specific Pcr ◽  
Resistant Strains ◽  
Xanthomonas Arboricola

Walnut bacterial blight caused by Xanthomonas arboricola pv. juglandis (Xaj) has serious repercussions for walnut production around the world. Between 2015 and 2017, disease samples were collected from six counties (Danjiangkou, Baokang, Suizhou, Shennongjia, Zigui, and Xingshan) in Hubei province, China. Fifty-nine Xaj strains were identified by morphology and specific PCR primers from 206 isolates. The genetic diversity of 60 Xaj strains (59 from Hubei plus one from Beijing) was evaluated by Multilocus Sequence Analysis (MLST), and their resistance to copper ion (Cu2+) treatment was determined. A Neighbor Joining phylogenetic dendrogram was constructed based on four sequences of housekeeping genes (atpD-dnaK-glnA-gyrB). Two groups of strains were identified whose clustering was consistent with that of glnA. The minimal inhibitory concentration of copper ion on representative Xaj strain DW3F3 (the first genome sequenced Xaj from China) was 115 μg/ml. Setting the copper resistant threshold value to 125 μg/ml, 47 and 13 strains were considered sensitive and resistant to Cu2+, respectively. Furthermore, five strains showed Cu2+ resistance at 270 μg/ml. Compared to the copB from sensitive strains, the copB gene in resistant strains had a 15-bp insertion and eight scattered single nucleotide polymorphisms. Interestingly, the clustering based on MLSA was distinct between Xaj copper ion resistant and sensitive strains.

scholarly journals WildTermitomycesSpecies Collected from Ondo and Ekiti States Are More Related to African Species as Revealed by ITS Region of rDNA

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Victor Olusegun Oyetayo
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Molecular Identification ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Its Sequence ◽  
African Countries ◽  
African Species ◽  
Its Sequence Analysis ◽  
Degree Of Similarity

Molecular identification of eighteenTermitomycesspecies collected from two states, Ondo and Ekiti in Nigeria was carried out using the internal transcribed spacer (ITS) region. The amplicons obtained from rDNA ofTermitomycesspecies were compared with existing sequences in the NCBI GenBank. The results of the ITS sequence analysis discriminated between all theTermitomycesspecies (obtained from Ondo and Ekiti States) andTermitomycessp. sequences obtained from NCBI GenBank. The degree of similarity of T1 to T18 to gene ofTermitomycessp. obtained from NCBI ranges between 82 and 99 percent.Termitomycesspecies from Garbon with ascension number AF321374 was the closest relative of T1 to T18 except T12 that has T. eurhizus and T. striatus as the closet relative. Phylogenetic tree generated with ITS sequences obtained from NCBI GenBank data revealed that T1 to T18 are more related toTermitomycesspecies indigenous to African countries such as Senegal, Congo, and Gabon.

scholarly journals Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species

2010 ◽  
Vol 60 (3) ◽  
pp. 696-703 ◽  
Author(s):  
Xiaoying Rong ◽  
Ying Huang
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Streptomyces Griseus ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Good Resolution ◽  
Species Definition ◽  
Genomic Species

Streptomyces griseus and related species form the biggest but least well-defined clade in the whole Streptomyces 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining Streptomyces systematics. In this investigation, strains of 18 additional S. griseus clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA–DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the S. griseus clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the S. griseus clade are considered to be later heterotypic synonyms of 11 genomic species: Streptomyces griseinus and Streptomyces mediolani as synonyms of Streptomyces albovinaceus; Streptomyces praecox as a synonym of Streptomyces anulatus; Streptomyces olivoviridis as a synonym of Streptomyces atroolivaceus; Streptomyces griseobrunneus as a synonym of Streptomyces bacillaris; Streptomyces cavourensis subsp. washingtonensis as a synonym of Streptomyces cyaneofuscatus; Streptomyces acrimycini, Streptomyces baarnensis, Streptomyces caviscabies and Streptomyces flavofuscus as synonyms of Streptomyces fimicarius; Streptomyces flavogriseus as a synonym of Streptomyces flavovirens; Streptomyces erumpens, ‘Streptomyces ornatus’ and Streptomyces setonii as synonyms of Streptomyces griseus; Streptomyces graminofaciens as a synonym of Streptomyces halstedii; Streptomyces alboviridis, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces luridiscabiei as synonyms of Streptomyces microflavus; and Streptomyces californicus and Streptomyces floridae as synonyms of Streptomyces puniceus.

scholarly journals Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

2014 ◽  
Vol 80 (17) ◽  
pp. 5503-5514 ◽  
Author(s):  
Christophe Habib ◽  
Armel Houel ◽  
Aurélie Lunazzi ◽  
Jean-François Bernardet ◽  
Anne Berit Olsen ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Multilocus Sequence Analysis ◽  
Fish Pathogens ◽  
Long Distance ◽  
Marine Aquaculture ◽  
Content Type ◽  
The Family ◽  
Cohesive Group

ABSTRACTThe genusTenacibaculum, a member of the familyFlavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogenTenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the speciesT. maritimumconstitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoringTenacibaculuminfections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related toT. dicentrarchi, a recently described species.

scholarly journals MOLECULAR IDENTIFICATION OF Pepper yellow leaf curl Indonesia virus ON CHILI PEPPER IN NUSA PENIDA ISLAND

2021 ◽  
Vol 21 (2) ◽  
pp. 97-102
Author(s):  
Dewa Gede Wiryangga Selangga ◽  
Listihani Listihani
Keyword(s):  
Sequence Analysis ◽  
Molecular Identification ◽  
Disease Incidence ◽  
Analysis Data ◽  
Chili Pepper ◽  
Yellow Leaf ◽  
Degenerate Primers ◽  
Disease Symptoms ◽  
Leaf Curl Disease ◽  
Leaf Curl

Molecular identification of Pepper yellow leaf curl Indonesia virus on chili pepper in Nusa Penida Island. Pepper yellow leaf curl Indonesia virus (PYLCV) has been reported as caused yellow leaf curl disease in Bali Island since early 2012. Dominant symptoms of PYLCV infection in chili pepper were yellowing, leaf curl, yellow mosaic, and mottle. Bemisia tabaci, has been known to vector on the case yellow leaf curl disease. Observations on the Nusa Penida Island in 2020 showed symptoms such as yellow leaf curl disease, however, identification of PYLCV in Nusa Penida Island has not been studied. Molecular identification was conducted using polymerase chain reaction and sequence analysis. Data collected in this study was disease symptoms and disease incidence. The results showed that dominant disease symptoms caused by virus from Nusa Penida were yellow mosaic, yellowing, and mottle. Universal DNA fragments of 912 bp were successfully amplified from 50 leaf samples using Begomovirus degenerate primers SPG 1 (5’-CCCCKGTGCGWRAATCCAT-3’) and SPG 2 (5’ATCCVAA YWTYCAGGGAGCT-3’). Sequence analysis showed that the isolate from Nusa Penida was a Pepper yellow leaf curl Indonesia virus with a 98–100% homology with several reference isolates.

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